Chromosome Research

, Volume 27, Issue 3, pp 153–165 | Cite as

Fluorescence in situ hybridization in plants: recent developments and future applications

  • Jiming JiangEmail author
Waldeyer-Flemming Special Collection


Fluorescence in situ hybridization (FISH) was developed more than 30 years ago and has been the most paradigm-changing technique in cytogenetic research. FISH has been used to answer questions related to structure, mutation, and evolution of not only individual chromosomes but also entire genomes. FISH has served as an important tool for chromosome identification in many plant species. This review intends to summarize and discuss key technical development and applications of FISH in plants since 2006. The most significant recent advance of FISH is the development and application of probes based on synthetic oligonucleotides (oligos). Oligos specific to a repetitive DNA sequence, to a specific chromosomal region, or to an entire chromosome can be computationally identified, synthesized in parallel, and fluorescently labeled. Oligo probes designed from conserved DNA sequences from one species can be used among genetically related species, allowing comparative cytogenetic mapping of these species. The advances with synthetic oligo probes will significantly expand the applications of FISH especially in non-model plant species. Recent achievements and future applications of FISH and oligo-FISH are discussed.


FISH Oligo-FISH Karyotype Chromosome Genome Evolution 



Bacterial artificial chromosome


Chromatin immunoprecipitation


Extrachromosomal circular DNA


Fluorescence in situ hybridization


Million years




Simple-sequence repeats



FISH images in Fig. 2 were developed by Guilherme Braz, Li He, Tao Zhang, and Pingdong Zhang.

Funding information

Cytogenetic research in the author’s lab has been supported by National Science Foundation (NSF) grants IOS-1444514 and MCB-1412948.


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© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.Department of Plant Biology, Department of HorticultureMichigan State UniversityEast LansingUSA

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